The Potters - on a four-match losing run in the Premier League and lying bottom of the table with just one point - had gone into the third-round tie at the Bet365 Stadium in need of a boost.
And they were the better team virtually throughout the contest against the Tigers.
superfly mercurial v black But after Marko Arnautovic's finely struck 24th-minute effort gave them the lead, they conceded late on in each half to end up crashing out, with a volley from Ryan Mason and then Markus Henriksen's finish at the death securing Hull a fourth-round trip to Bristol City.
magista obra orange Asked afterwards if he felt hard done by, Hughes said: "To say the least - it would be a little bit of an understatement to say that.
"We have just gone through 90 minutes of a totally dominant performance, really.
"In the first half I think we started really intense, causing Hull a lot of problems, and we scored a great opening goal, a fantastic strike from Marko.
mercurial vapor v black "Then (Hull scored) with probably their only attack of the first half - you have to say it is a fantastic finish.
ace 16 purecontrol cleats "We're scratching our heads at that point, wondering how we are going in at half-time on level terms, but we came out in the second half with exactly the same intent and were continually asking questions of Hull, who looked content to just to soak pressure up and get through to penalties, it seemed.
"So to lose it right at the end is a little bit hard to take, I have to say, because I think the performance merited a win.
"We were the side that were trying to make things happen and creating chances, but unfortunately it didn't lead to us progressing in the competition, which is what we wanted."
Stoke's next match is Saturday's Premier League home clash with West Brom, managed by ex-Potters boss Tony Pulis.
x 16 purechao black Hughes said: "The key now is we have a big game at the weekend and we have to pick ourselves up.
"I thought there were good elements to our play tonight, so that is an encouragement for us.
"It was an undeserved victory for Hull, I felt. But that is what they have got, so we have to dust ourselves down and get going again."
